Spoilers

Who or what is this "Other M" that is referenced in the game's title? Is there anywhere this is stated definitively (or pretty clearly implied) in the game? I've finished the whole game, including the return to the bottle ship to get Adam's helmet, and I don't remember anything. (I have not played on hard mode though.)

I originally thought it meant the other metroids that were being bio-engineered to be cold-resistant. But then I thought it must be referring to something other than metroids ("Metroid" is already in the title, so the other "M" must be something else), so now I'm going on the theory that MB is the other "M". But I'd love to know one way or the other if there is any clear answer I missed.

There are a startling number of similarities between Other M and Fusion. I've seen it said that Other M is a remake of Fusion, in which case the "Other M" monicker would indicate an "alternate" timeline. ("Other Metroid Fusion" But as this is nothing but speculation on several fans parts...)
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Raven Dreamer♦Sep 19 '10 at 4:07

I don't have an answer but I don't think it follows that just because Metroid is already in the title means that M must mean something else. In fact logically speaking it could likely indicate otherwise, that it DOES mean Metroid because it's already in the title and they didn't want to sound repetitive so they just made it M.
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ioSamuraiSep 19 '10 at 14:42

@RavenDreamer Fusion is the last game in the Metroid timeline. Other M takes place between Super Metroid and Fusion.
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CyberSkullJun 26 '13 at 10:14

As I understood it, it alludes to the plot twist late in the game when we learn "Madeline Bergman" is in fact "MB", and another woman altogether is the real Madeline Bergman. Both share initials, each beginning with M.

They could have called it Metroid Other MB, but that would have spoiled the plot.